Harbours, which are often characterised by anthropogenic stress in combination with intensive international ship traffic, tend to be very susceptible to aquatic invasions. Since alien macrocrustaceans are known to be very successful across many European waters, a study was made on their distribution and impact in the four Belgian coastal harbours (Nieuwpoort, Ostend, Blankenberge and Zeebrugge). Biological and physical–chemical data were gathered at 43 sampling sites distributed along a salinity gradient in the four harbours. One-fourth of all crustacean species recorded were alien and represented on average 30% of the total macrocrustacean abundance and 65% of the total macrocrustacean biomass. The large share of alien crustaceans in the total macrocrustacean biomass was mainly due to several large alien crab species. Most alien species were found in the oligohaline zone, whereas the number of indigenous species slightly increased with increasing salinity. The low number of indigenous species present at low salinities was probably not only caused by salinity, but also by the lower water quality in this salinity range. Based on the site-specific biocontamination index (SBCI), which was used to assess the ecological water quality, the harbour of Nieuwpoort and Ostend scored best and were classified as good, indicating the limited abundance and the low number of alien macrocrustaceans. Sampling locations situated more inland generally had a higher SBCI and a lower ecological water quality. Zeebrugge and Blankenberge were characterised by a severe biocontamination. For Zeebrugge, this is probably related to the intensive transcontinental commercial ship traffic, whereas for Blankenberge, this could be due to introduction of alien species via recreational crafts or due to its geographical location in the proximity of Zeebrugge. Consistent monitoring of estuarine regions and harbours, which are seen as hotspots for introductions, could help in understanding and predicting the impact of alien species on native biota.